SAXSdb — 5nmv

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tissue factor pathway inhibitor

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain K； UniProt 29–107	Not recorded	Fab light chain × 1 Fab heavy chain × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20 % PEG 3350 200 mM Potassium formate	Resolution 1.65 Å R-free 0.202

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5NMV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ADZ THE SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR, NMR, 30 STRUCTURES Deposited 1997-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–182（76 aa） Fragment：FACTOR XA-BINDING DOMAIN (DOMAIN II)	Mutation：N-TERMINAL INS(DYKDDDDKL)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；310 K；Pressure 1	Resolution not provided
1IRH The Solution Structure of The Third Kunitz Domain of Tissue Factor Pathway Inhibitor Deposited 2001-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 210–270（61 aa） Fragment：the third kunitz domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1mM the third kunitz domain of tissue factor pathway inhibitor U-15N; 20mM Na-phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM the third kunitz domain of tissue factor pathway inhibitor U-15N, 13C; 20mM Na-phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1TFX COMPLEX OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR WITH PORCINE TRYPSIN Deposited 1997-01-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 121–178（58 aa） Fragment：FACTOR XA-BINDING DOMAIN, DOMAIN II	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å
1TFX COMPLEX OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR WITH PORCINE TRYPSIN Deposited 1997-01-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 121–178（58 aa） Fragment：FACTOR XA-BINDING DOMAIN, DOMAIN II	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å
4DTG Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model Deposited 2012-02-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 119–178（60 aa） Fragment：Kunitz-type protease inhibitor domain 2 (UNP residues 119-178)	Not recorded	GOL GLYCEROL × 10 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PGE TRIETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；295 K；0.05 M CALCIUM CHLORIDE, 0.1 M MES, pH 6.0, 45% V/V PEG 200, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.236
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
7V1N Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI Deposited 2021-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–251（251 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9P0X Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted) Deposited 2025-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 40–107（68 aa）	Not recorded	MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 BGC beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TFPI1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain K； PDBConstruct 8–86； UniProt 29–107

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5nmv
Deposition date deposition_date	2017-04-07
Structure title title	Crystal structure of 2F22 Fab fragment against TFPI1
Keywords keywords	Fab, immune system; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.20 Å
Radius of gyration Rg (electron density) rg_electron	26.55 Å
Forward intensity I(0) i0	50445700.00
Molecular weight molecular_weight	54484.0 kDa
Excluded volume excluded_volume	67794 Å³
Envelope volume envelope_volume	84521 Å³
Hydration-shell volume shell_volume	27404 Å³
Envelope diameter envelope_diameter	95.4 Å
Shell Rg shell_rg	32.97 Å
Envelope Rg envelope_rg	26.40 Å
Shape Rg shape_rg	26.52 Å
Total Rg total_rg	27.31 Å
Total atoms total_atoms	7544
Residues n_residues	496
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.2 Å
Rg (real space) rg_real	27.30 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	5.0450e+07
I(0) uncertainty (real space) i0_real_error	7.5330e+05
Rg (reciprocal space) rg_reciprocal	27.27 Å
I(0) (reciprocal space) i0_reciprocal	50440000.0000
Solution quality estimate total_estimate	0.8846
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.422
Kurtosis Kurtosis kurtosis	-0.334
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8263000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.953

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Fab light chain
Molecular weight formula_weight	23242.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	8216

GIVMTQSQKFMSTTVGDRVSITCKASQSVGPAVAWYQQKPGQSPKLLIYSASNRYTGVPDRFTGSGSGADFTLTISNLHSEDLADYFCQQYTSYPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus
NCBI Class编号 ncbi_taxonomy_id	10088
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	23814.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLAVIWRGGSIDYNAAFMSRLSITKDNSKSQVFFKMNSLQADDTAIYYCAKNSHGNYVGYAMDYWGQGTSVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESK

来源 Source

来源生物 organism	Mus
NCBI Class编号 ncbi_taxonomy_id	10088
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Tissue factor pathway inhibitor
Molecular weight formula_weight	9797.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

GSSGSSGDSEEDEEHTIITDTELPPLKLMHSFCAFKADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEECKKMCTRD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	489

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5nmvk_
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5nmvH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nmvK00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	5nmvL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nmvL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	89.010 Å
Unit-cell length b length_b	66.660 Å
Unit-cell length c length_c	106.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	27.642 Å
R factor r_factor	0.1766
R_work r_work	0.1752
R_free r_free	0.2022

fit	/app/data/saxs_computation/nm/5nmv/5nmv.fit
pddf	/app/data/pr_computation/nm/5nmv/5nmv.pr.out
profile	/app/data/saxs_computation/nm/5nmv/5nmv.dat

Crystal structure of 2F22 Fab fragment against TFPI1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tissue factor pathway inhibitor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)